Job ID = 5791627 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 1900-01-00T00:00:00 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) ) 2020-04-22T00:54:43 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) ) 2020-04-22T00:54:43 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T00:54:43 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 32,219,650 reads read : 64,439,300 reads written : 64,439,300 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:23 32219650 reads; of these: 32219650 (100.00%) were paired; of these: 2465779 (7.65%) aligned concordantly 0 times 26125405 (81.09%) aligned concordantly exactly 1 time 3628466 (11.26%) aligned concordantly >1 times ---- 2465779 pairs aligned concordantly 0 times; of these: 54262 (2.20%) aligned discordantly 1 time ---- 2411517 pairs aligned 0 times concordantly or discordantly; of these: 4823034 mates make up the pairs; of these: 4555515 (94.45%) aligned 0 times 211029 (4.38%) aligned exactly 1 time 56490 (1.17%) aligned >1 times 92.93% overall alignment rate Time searching: 00:16:23 Overall time: 00:16:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 28 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 18185750 / 29762226 = 0.6110 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:28:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 10:28:18: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:28:18: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:28:22: 1000000 INFO @ Wed, 22 Apr 2020 10:28:27: 2000000 INFO @ Wed, 22 Apr 2020 10:28:31: 3000000 INFO @ Wed, 22 Apr 2020 10:28:35: 4000000 INFO @ Wed, 22 Apr 2020 10:28:40: 5000000 INFO @ Wed, 22 Apr 2020 10:28:44: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:28:49: 7000000 INFO @ Wed, 22 Apr 2020 10:28:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 10:28:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:28:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:28:53: 8000000 INFO @ Wed, 22 Apr 2020 10:28:53: 1000000 INFO @ Wed, 22 Apr 2020 10:28:58: 9000000 INFO @ Wed, 22 Apr 2020 10:28:58: 2000000 INFO @ Wed, 22 Apr 2020 10:29:02: 10000000 INFO @ Wed, 22 Apr 2020 10:29:03: 3000000 INFO @ Wed, 22 Apr 2020 10:29:07: 11000000 INFO @ Wed, 22 Apr 2020 10:29:07: 4000000 INFO @ Wed, 22 Apr 2020 10:29:11: 12000000 INFO @ Wed, 22 Apr 2020 10:29:12: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:29:16: 13000000 INFO @ Wed, 22 Apr 2020 10:29:16: 6000000 INFO @ Wed, 22 Apr 2020 10:29:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 10:29:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:29:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:29:20: 14000000 INFO @ Wed, 22 Apr 2020 10:29:21: 7000000 INFO @ Wed, 22 Apr 2020 10:29:22: 1000000 INFO @ Wed, 22 Apr 2020 10:29:25: 15000000 INFO @ Wed, 22 Apr 2020 10:29:25: 8000000 INFO @ Wed, 22 Apr 2020 10:29:27: 2000000 INFO @ Wed, 22 Apr 2020 10:29:30: 16000000 INFO @ Wed, 22 Apr 2020 10:29:30: 9000000 INFO @ Wed, 22 Apr 2020 10:29:31: 3000000 INFO @ Wed, 22 Apr 2020 10:29:34: 17000000 INFO @ Wed, 22 Apr 2020 10:29:35: 10000000 INFO @ Wed, 22 Apr 2020 10:29:36: 4000000 INFO @ Wed, 22 Apr 2020 10:29:39: 18000000 INFO @ Wed, 22 Apr 2020 10:29:39: 11000000 INFO @ Wed, 22 Apr 2020 10:29:41: 5000000 INFO @ Wed, 22 Apr 2020 10:29:44: 19000000 INFO @ Wed, 22 Apr 2020 10:29:44: 12000000 INFO @ Wed, 22 Apr 2020 10:29:45: 6000000 INFO @ Wed, 22 Apr 2020 10:29:48: 20000000 INFO @ Wed, 22 Apr 2020 10:29:48: 13000000 INFO @ Wed, 22 Apr 2020 10:29:50: 7000000 INFO @ Wed, 22 Apr 2020 10:29:53: 21000000 INFO @ Wed, 22 Apr 2020 10:29:53: 14000000 INFO @ Wed, 22 Apr 2020 10:29:54: 8000000 INFO @ Wed, 22 Apr 2020 10:29:57: 22000000 INFO @ Wed, 22 Apr 2020 10:29:58: 15000000 INFO @ Wed, 22 Apr 2020 10:29:59: 9000000 INFO @ Wed, 22 Apr 2020 10:30:02: 23000000 INFO @ Wed, 22 Apr 2020 10:30:02: 16000000 INFO @ Wed, 22 Apr 2020 10:30:04: 10000000 INFO @ Wed, 22 Apr 2020 10:30:04: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:30:04: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:30:04: #1 total tags in treatment: 11571952 INFO @ Wed, 22 Apr 2020 10:30:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:30:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:30:05: #1 tags after filtering in treatment: 8292027 INFO @ Wed, 22 Apr 2020 10:30:05: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Apr 2020 10:30:05: #1 finished! INFO @ Wed, 22 Apr 2020 10:30:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:30:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:30:05: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:30:05: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 10:30:05: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:30:07: 17000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:30:09: 11000000 INFO @ Wed, 22 Apr 2020 10:30:11: 18000000 INFO @ Wed, 22 Apr 2020 10:30:13: 12000000 INFO @ Wed, 22 Apr 2020 10:30:16: 19000000 INFO @ Wed, 22 Apr 2020 10:30:18: 13000000 INFO @ Wed, 22 Apr 2020 10:30:21: 20000000 INFO @ Wed, 22 Apr 2020 10:30:23: 14000000 INFO @ Wed, 22 Apr 2020 10:30:25: 21000000 INFO @ Wed, 22 Apr 2020 10:30:27: 15000000 INFO @ Wed, 22 Apr 2020 10:30:30: 22000000 INFO @ Wed, 22 Apr 2020 10:30:32: 16000000 INFO @ Wed, 22 Apr 2020 10:30:34: 23000000 INFO @ Wed, 22 Apr 2020 10:30:36: 17000000 INFO @ Wed, 22 Apr 2020 10:30:37: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:30:37: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:30:37: #1 total tags in treatment: 11571952 INFO @ Wed, 22 Apr 2020 10:30:37: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:30:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:30:37: #1 tags after filtering in treatment: 8292027 INFO @ Wed, 22 Apr 2020 10:30:37: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Apr 2020 10:30:37: #1 finished! INFO @ Wed, 22 Apr 2020 10:30:37: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:30:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:30:37: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:30:37: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 10:30:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:30:41: 18000000 INFO @ Wed, 22 Apr 2020 10:30:45: 19000000 INFO @ Wed, 22 Apr 2020 10:30:50: 20000000 INFO @ Wed, 22 Apr 2020 10:30:54: 21000000 INFO @ Wed, 22 Apr 2020 10:30:58: 22000000 INFO @ Wed, 22 Apr 2020 10:31:03: 23000000 INFO @ Wed, 22 Apr 2020 10:31:05: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:31:05: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:31:05: #1 total tags in treatment: 11571952 INFO @ Wed, 22 Apr 2020 10:31:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:31:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:31:05: #1 tags after filtering in treatment: 8292027 INFO @ Wed, 22 Apr 2020 10:31:05: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Apr 2020 10:31:05: #1 finished! INFO @ Wed, 22 Apr 2020 10:31:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:31:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:31:06: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:31:06: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 10:31:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409595/SRX7409595.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。